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Series GSE179796 Query DataSets for GSE179796
Status Public on Dec 01, 2021
Title Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. Here we show that without histone H1, RdDM enters heterochromatin, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.
 
Overall design Bisulfite and RNA sequencing was performed using h1cmt2, h1cmt2shh1, h1cmt2cmt3 plants (1-2 replicates) to examine the effect of H1, non-CG DNA methylation and SHH1 on RNA-directed DNA methylation activity. sRNA-seq was performed using wt, h1, ddm1, h1ddm1, cmt2cmt3, h1cmt2cmt3, met1, and h1met1 plants (3 replicates, except for met1 and h1met1) to examine the effect of H1, non-CG DNA methylation on 24 nt sRNA expression. To explore H3K9me1 and H3K9me2 distribution in wt, h1, ddm1, h1ddm1, cmt2cmt3, and h1cmt2cmt3, antibody against H3K9me1 and H3K9me2 were used to enrich chromatin bound to modified histones.
 
Contributor(s) Choi J, Lyons DB
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Submission date Jul 09, 2021
Last update date Dec 03, 2021
Contact name Jaemyung Choi
E-mail(s) choij@nbi.ac.uk
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Daniel Zilberman
Street address Norwich Research Park
City Norwich
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platforms (2)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (62)
GSM5434256 cmt2_bisulfite
GSM5434257 cmt2cmt3_bisulfite
GSM5434258 h1cmt2_bisulfite_rep1
Relations
BioProject PRJNA745095
SRA SRP327627

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE179796_RAW.tar 1.5 Gb (http)(custom) TAR (of BW, GFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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